docs: linked the wiki page explaining FLINT modules

docs/Understanding-FLINT/moja-flint/modules.rst

@@ -1,90 +1,95 @@
-Modules
-======================
-
-What is a module?
------------------
-
-A module is a self-contained set of operations that determine the state
-of, or change in, variables across a specified period for a single
-Simulation Unit in direct response to event notifications from the FLINT
-core system (Unit Controller). For example, the empirical forest growth
-module includes all the operations required to simulate biomass
-accumulation.
-
-How do modules operate?
------------------------
-
-Each module reads (or is provided with – see Unit Controller)
-information about the current state variables and the data required to
-update the state variables, such as climate data or information about
-disturbances to simulate. Each module then performs the required
-calculations and returns information about the updates to apply to each
-state variable and C pools. For state variables such as age or height,
-modules can return the updated value, but for all carbon pools and other
-fluxes, the module returns the proposed operations' array (sparse
-matrix). This array will include information about the source pool, the
-sink pool, and the amount (Mg ha-1 per time step) of the flux.
-Module-specific metadata regarding units and time step size is also
-required. This information is all returned to the Unit Controller.
-
-In terms of the FLINT programming framework, there are internal and
-external modules. The internal modules tend to be generic utility
-modules, for example, for producing output tables. At the same time,
-external modules are regionally or nationally specific. By using modules
-and separating the generic and specific, FLINT's framework remains
-highly flexible, and new modules can be 'plugged in' as they are
-developed. Standard modules in FLINT
-
-The FLINT includes six standard modules for simulating changes in forest
-and crop systems, including changes in soil carbon. These modules each
-run for all simulations at a monthly step interval (see Temporal
-Distribution) and include:
-
--  Empirical forest growth module
--  Hybrid forest growth module
--  WOFOST crop growth module
--  Turnover module
--  Decomposition module
--  RothC soil carbon module
-
-Modules for disturbance events
-------------------------------
-
-Disturbance events occur intermittently (rather than for every step in a
-simulation) and affect carbon stocks. Disturbance events include natural
-and anthropogenic events, including fire, harvesting, plowing, and
-fertilizer application (Table 2). While disturbance events are modules
-within FLINT, they are referred to separately as they are not run on
-every simulation, as are the modules mentioned above. FLINT can use
-tabular or spatial data to account for disturbance events as a minimum
-FLINT needs the date of the disturbance and the disturbance type. Where
-tabular data is used, information is also needed for the amount (or
-proportion) affected, the units the disturbance event is reported in
-(area, carbon, etc.), and any eligibility criteria (i.e., Simulation
-Unit characteristics that the event is allowed to affect). We can use
-this information to attribute the disturbance event to Simulation Units
-using pre-determined criteria (e.g., randomly, weighted, or based on a
-unit characteristic).
-
-The following are disturbance events included in FLINT. Carbon pool
-events directly affect one or more carbon pools, while non-carbon pool
-events indirectly affect one or more non-carbon pools.
-
-Carbon pool events
-~~~~~~~~~~~~~~~~~~
-
--  Fire
--  Harvest
--  Herbicide
--  Plough
--  Debris mulching
--  Grazing
--  Organic matter additions
--  Planting
-
-Non-Carbon Events
-~~~~~~~~~~~~~~~~~
-
--  Irrigation
--  Fertilizer application
--  Compaction
+Modules
+======================
+
+What is a module?
+-----------------
+
+A module is a self-contained set of operations that determine the state
+of, or change in, variables across a specified period for a single
+Simulation Unit in direct response to event notifications from the FLINT
+core system (Unit Controller). For example, the empirical forest growth
+module includes all the operations required to simulate biomass
+accumulation.
+
+How do modules operate?
+-----------------------
+
+Each module reads (or is provided with – see Unit Controller)
+information about the current state variables and the data required to
+update the state variables, such as climate data or information about
+disturbances to simulate. Each module then performs the required
+calculations and returns information about the updates to apply to each
+state variable and C pools. For state variables such as age or height,
+modules can return the updated value, but for all carbon pools and other
+fluxes, the module returns the proposed operations' array (sparse
+matrix). This array will include information about the source pool, the
+sink pool, and the amount (Mg ha-1 per time step) of the flux.
+Module-specific metadata regarding units and time step size is also
+required. This information is all returned to the Unit Controller.
+
+In terms of the FLINT programming framework, there are internal and
+external modules. The internal modules tend to be generic utility
+modules, for example, for producing output tables. At the same time,
+external modules are regionally or nationally specific. By using modules
+and separating the generic and specific, FLINT's framework remains
+highly flexible, and new modules can be 'plugged in' as they are
+developed. Standard modules in FLINT
+
+The FLINT includes six standard modules for simulating changes in forest
+and crop systems, including changes in soil carbon. These modules each
+run for all simulations at a monthly step interval (see Temporal
+Distribution) and include:
+
+-  Empirical forest growth module
+-  Hybrid forest growth module
+-  WOFOST crop growth module
+-  Turnover module
+-  Decomposition module
+-  RothC soil carbon module
+
+Refer on our `modules documentation`_.
+
+.. _modules documentation: https://github.com/moja-global/FLINT/wiki/3.4-Module-Science
+
+
+Modules for disturbance events
+------------------------------
+
+Disturbance events occur intermittently (rather than for every step in a
+simulation) and affect carbon stocks. Disturbance events include natural
+and anthropogenic events, including fire, harvesting, plowing, and
+fertilizer application (Table 2). While disturbance events are modules
+within FLINT, they are referred to separately as they are not run on
+every simulation, as are the modules mentioned above. FLINT can use
+tabular or spatial data to account for disturbance events as a minimum
+FLINT needs the date of the disturbance and the disturbance type. Where
+tabular data is used, information is also needed for the amount (or
+proportion) affected, the units the disturbance event is reported in
+(area, carbon, etc.), and any eligibility criteria (i.e., Simulation
+Unit characteristics that the event is allowed to affect). We can use
+this information to attribute the disturbance event to Simulation Units
+using pre-determined criteria (e.g., randomly, weighted, or based on a
+unit characteristic).
+
+The following are disturbance events included in FLINT. Carbon pool
+events directly affect one or more carbon pools, while non-carbon pool
+events indirectly affect one or more non-carbon pools.
+
+Carbon pool events
+~~~~~~~~~~~~~~~~~~
+
+-  Fire
+-  Harvest
+-  Herbicide
+-  Plough
+-  Debris mulching
+-  Grazing
+-  Organic matter additions
+-  Planting
+
+Non-Carbon Events
+~~~~~~~~~~~~~~~~~
+
+-  Irrigation
+-  Fertilizer application
+-  Compaction